In this study, we reported the outcomes of hematopoietic stem cell transplantation (HSCT) as a treatment modality for pediatric patients admitted over the past 20 years in a single institute. From January 1989 to January 2007, 26 patients with a median age of 8 years underwent 14 matched sibling donor (MSD) and 12 alternative donor (AD) transplantations. Two patients received second transplantation successfully after primary graft failure and late graft rejection. Two patients who received transplantation from matched unrelated donors (MUD) died of sepsis, and one of them also had a graft failure at death. The overall 5-year survival rate was 92.1%: 83.3% for AD transplantation and 100% for MSD transplantation. Grade II acute graft versus host disease (GVHD) developed in 3 patients, and extensive chronic GVHD developed in 2 patients. An interval of more than 6 months from diagnosis to transplantation was the major poor prognostic factor for our patients' survival. Thus, in our experience, HSCT from a MSD remains the first choice of treatment for pediatric patients with severe aplastic anemia. For patients without MSD, transplantation from an AD can also result in long-term survival. Earlier transplantation after diagnosis can also result in better outcomes.